Comments (5)
Thanks for filing an issue, but I'm not sure what you're asking for.
Our disk
key specifies the minimum storage size for a task running on a DNAnexus/Azure VM. It's expected for other backends to ignore this value (keys in the runtime
section of a WDL task can be backend specific, so being ignored by alternate backends is expected. For example, we often run our pipeline on our local LSF cluster, which similarly logs a message about ignoring the disk
key).
I was unable to find GCP documentation about the disks
key you are referring to, but I'm guessing it means something other than what disk
on DNAnexus/Azure means.
Are the workflows failing, or just logging this message? If they're failing, what is the specific error causing the failure?
from workflows.
Thanks for the quick response. Ok, given the WARNING it is probably ignored and won't cause issues.
I put in my options file:
"default_runtime_attributes": {
"zones": "us-central1-a us-central1-b us-central1-c us-central1-f",
"memory": "16G",
"disks": "local-disk 100 SSD"
}
But I see in the logs:
Adjusting boot disk size to 12 GB: 10 GB (runtime attributes) + 1 GB (user command image) + 1 GB
Which indicates to me either the 'disk' is ignored or my 'disks' is ignored.
from workflows.
Perhaps this is a Cromwell issue.
from workflows.
Sorry, I don't think anyone on this team has experience with GCP. This sounds like a Cromwell configuration issue on your end that I don't think we're equipped to handle.
However the below documentation links seem extensive, and may help you:
https://cromwell.readthedocs.io/en/stable/tutorials/PipelinesApi101/
https://cromwell.readthedocs.io/en/stable/backends/Google/
from workflows.
Ok. I can close. Thanks for looking at it.
from workflows.
Related Issues (13)
- our WDL files are too long
- Style Guide rules under review
- Split tasks to a new repository HOT 1
- NGSderive step assumes plain text HOT 1
- Picard sort task fails for non-coordinate sorts
- Remove duplicate marking HOT 1
- tools/htseq: Add override or fix htseq-count max-reads-in-buffer option HOT 3
- workflows/rnaseq: 2.1.0 is not backward compatible with 2.0.0 HOT 3
- Add CI for checking all tasks pull current docker images
- Modularize QC HOT 2
- investigate appropriate `disk_size`s HOT 1
- WDL/1.1
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from workflows.